N - mixture models by species
modelling N by site to get relative abundance
abundance by site will be used as a cov on predator occupancy
7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ
Species: Â Â Â Â AmericanPika
Detections by Year:
|
Yr
|
2016
|
2017
|
2018
|
2019
|
2020
|
|
sites
|
19
|
31
|
19
|
32
|
26
|
|
detections
|
5
|
10
|
0
|
24
|
20
|
|
N.dot.model
|
2
|
5
|
0
|
11
|
6
|
WAIC
Models by WAIC:
|
model
|
description
|
WAIC
|
N.total.est
|
|
fm7
|
counts
|
3.889332
|
108
|
|
fm4
|
lure + jdt
|
358.924599
|
24
|
|
fm2
|
jdt
|
359.814351
|
25
|
|
fm6
|
lure + jdt + jdtSq
|
360.277323
|
24
|
|
fm5
|
jdt + jdtSq
|
360.763399
|
25
|
|
fm3
|
lure
|
368.539468
|
25
|
|
fm1
|
dot
|
370.195910
|
24
|
Model summaries:
model: fm1
summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
p[1]
|
NA
|
8453
|
0.131
|
0.116
|
0.04
|
0.21
|
0
|
1.0009
|
|
p[2]
|
NA
|
6013
|
0.074
|
0.062
|
0.03
|
0.12
|
0
|
1.0009
|
|
p[3]
|
NA
|
10000
|
0.488
|
0.272
|
0.00
|
0.88
|
0
|
0.9843
|
|
p[4]
|
NA
|
6132
|
0.060
|
0.055
|
0.03
|
0.09
|
0
|
1.001
|
|
p[5]
|
NA
|
7934
|
0.127
|
0.124
|
0.08
|
0.17
|
0
|
1.001
|
|
lambda[1]
|
NA
|
8919
|
0.123
|
0.066
|
0.01
|
0.24
|
0
|
0.9932
|
|
lambda[2]
|
NA
|
4129
|
0.243
|
0.169
|
0.05
|
0.41
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[4]
|
NA
|
5803
|
0.503
|
0.423
|
0.22
|
0.76
|
0
|
1.001
|
|
lambda[5]
|
NA
|
10000
|
0.273
|
0.226
|
0.09
|
0.44
|
0
|
1.001
|
|
N[121]
|
NA
|
10092
|
0.033
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[63]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[107]
|
NA
|
9373
|
0.004
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[39]
|
NA
|
8014
|
0.073
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[88]
|
NA
|
9187
|
0.085
|
err
|
0.00
|
0.00
|
err
|
err
|
p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[121]

N[63]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[107]

N[39]

N[88]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
jdt
|
8406
|
0.448
|
0.439
|
0.22
|
0.67
|
0.00618
|
1.0004
|
|
alpha0
|
NA
|
6449
|
-2.611
|
-2.607
|
-2.93
|
-2.29
|
0
|
1.001
|
|
lambda[1]
|
NA
|
10000
|
0.127
|
0.07
|
0.01
|
0.24
|
0
|
0.9939
|
|
lambda[2]
|
NA
|
10000
|
0.222
|
0.17
|
0.06
|
0.37
|
0
|
1.0008
|
|
lambda[3]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[4]
|
NA
|
10648
|
0.417
|
0.391
|
0.20
|
0.62
|
0
|
1.001
|
|
lambda[5]
|
NA
|
9240
|
0.359
|
0.294
|
0.13
|
0.57
|
0
|
1.001
|
|
N[105]
|
NA
|
9473
|
0.029
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[83]
|
NA
|
10107
|
0.079
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[107]
|
NA
|
9739
|
0.028
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[101]
|
NA
|
8248
|
0.012
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[119]
|
NA
|
10000
|
0.108
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[105]

N[83]

N[107]

N[101]

N[119]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
lure
|
10175
|
-0.113
|
-0.095
|
-0.36
|
0.11
|
0.76814
|
0.7752
|
|
alpha0
|
NA
|
7183
|
-2.463
|
-2.45
|
-2.75
|
-2.17
|
0
|
1.001
|
|
lambda[1]
|
NA
|
10000
|
0.131
|
0.073
|
0.01
|
0.25
|
0
|
0.9939
|
|
lambda[2]
|
NA
|
10000
|
0.206
|
0.151
|
0.05
|
0.34
|
0
|
1.0009
|
|
lambda[3]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[4]
|
NA
|
9188
|
0.413
|
0.373
|
0.19
|
0.61
|
0
|
1.001
|
|
lambda[5]
|
NA
|
9146
|
0.330
|
0.266
|
0.12
|
0.53
|
0
|
1.001
|
|
N[76]
|
NA
|
9698
|
0.078
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[55]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[58]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[2]
|
NA
|
10000
|
0.021
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[100]
|
NA
|
9782
|
0.015
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[76]

N[55]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[58]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[2]

N[100]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
6528
|
-0.409
|
-0.421
|
-0.68
|
-0.13
|
0.0605
|
0.9947
|
|
alpha[2]
|
julianDt
|
5904
|
0.615
|
0.608
|
0.35
|
0.86
|
0
|
1.001
|
|
alpha0
|
NA
|
4550
|
-2.709
|
-2.705
|
-3.07
|
-2.35
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9103
|
0.117
|
0.061
|
0.01
|
0.23
|
0
|
0.9943
|
|
lambda[2]
|
NA
|
9644
|
0.204
|
0.159
|
0.05
|
0.34
|
0
|
1.0008
|
|
lambda[3]
|
NA
|
9247
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[4]
|
NA
|
8955
|
0.428
|
0.402
|
0.21
|
0.64
|
0
|
1.001
|
|
lambda[5]
|
NA
|
5738
|
0.473
|
0.366
|
0.16
|
0.77
|
0
|
1.001
|
|
N[34]
|
NA
|
10000
|
0.019
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[125]
|
NA
|
10000
|
0.452
|
0
|
0.00
|
1.00
|
1
|
err
|
|
N[36]
|
NA
|
9284
|
0.021
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[105]
|
NA
|
8658
|
0.105
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[14]
|
NA
|
8077
|
0.009
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[34]

N[125]

N[36]

N[105]

N[14]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
julianDt
|
2240
|
0.212
|
0.193
|
-0.21
|
0.64
|
0.78346
|
0.7802
|
|
alpha[2]
|
julianDtSq
|
2197
|
0.238
|
0.253
|
-0.14
|
0.60
|
0.61391
|
0.8431
|
|
alpha0
|
NA
|
7177
|
-2.659
|
-2.633
|
-2.97
|
-2.32
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9696
|
0.136
|
0.072
|
0.01
|
0.26
|
0
|
0.9934
|
|
lambda[2]
|
NA
|
10650
|
0.218
|
0.169
|
0.06
|
0.37
|
0
|
1.0008
|
|
lambda[3]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[4]
|
NA
|
10175
|
0.413
|
0.376
|
0.20
|
0.61
|
0
|
1.001
|
|
lambda[5]
|
NA
|
8986
|
0.370
|
0.302
|
0.14
|
0.59
|
0
|
1.001
|
|
N[51]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[18]
|
NA
|
10022
|
0.020
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[108]
|
NA
|
10000
|
0.021
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[31]
|
NA
|
10000
|
0.014
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[59]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[51]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[18]

N[108]

N[31]

N[59]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

julian date relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
6082
|
-0.402
|
-0.384
|
-0.68
|
-0.11
|
0.06838
|
0.9913
|
|
alpha[2]
|
julianDt
|
2289
|
0.434
|
0.349
|
-0.04
|
0.87
|
0.31698
|
0.9382
|
|
alpha[3]
|
julianDtSq
|
2288
|
0.186
|
0.216
|
-0.20
|
0.55
|
0.71535
|
0.7844
|
|
alpha0
|
NA
|
4530
|
-2.749
|
-2.738
|
-3.11
|
-2.37
|
0
|
1.001
|
|
lambda[1]
|
NA
|
10000
|
0.123
|
0.075
|
0.00
|
0.23
|
0
|
0.994
|
|
lambda[2]
|
NA
|
9588
|
0.203
|
0.149
|
0.05
|
0.34
|
0
|
1.0008
|
|
lambda[3]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[4]
|
NA
|
8890
|
0.422
|
0.368
|
0.20
|
0.62
|
0
|
1.001
|
|
lambda[5]
|
NA
|
5724
|
0.484
|
0.355
|
0.16
|
0.78
|
0
|
1.001
|
|
N[97]
|
NA
|
10000
|
0.015
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[12]
|
NA
|
9555
|
0.009
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[70]
|
NA
|
10000
|
0.234
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[49]
|
NA
|
10000
|
0.007
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[43]
|
NA
|
10000
|
0.004
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[97]

N[12]

N[70]

N[49]

N[43]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
counts
|
8863
|
6.601
|
5.766
|
4.57
|
8.64
|
0
|
1.001
|
|
alpha0
|
NA
|
9717
|
-7.644
|
-7.406
|
-9.21
|
-5.96
|
0
|
1.001
|
|
lambda[1]
|
NA
|
4197
|
0.915
|
0.518
|
0.04
|
1.75
|
0
|
0.9931
|
|
lambda[2]
|
NA
|
4909
|
0.921
|
0.647
|
0.22
|
1.59
|
0
|
1.0007
|
|
lambda[3]
|
NA
|
1580
|
0.006
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[4]
|
NA
|
8177
|
0.974
|
0.91
|
0.46
|
1.46
|
0
|
1.001
|
|
lambda[5]
|
NA
|
6460
|
0.940
|
0.757
|
0.30
|
1.56
|
0
|
1.0009
|
|
N[56]
|
NA
|
1703
|
0.005
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[15]
|
NA
|
7057
|
0.905
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[27]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[35]
|
NA
|
7512
|
0.884
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[117]
|
NA
|
9099
|
0.914
|
0
|
0.00
|
2.00
|
1
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[56]

N[15]

N[27]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[35]

N[117]

alpha relationship
